Presentation: Patient with carcinoma of unknown primary

A 55-year-old woman is admitted with abdominal pain, weight loss and shortness of breath. Imaging reveals multiple sites of metastatic disease but no obvious primary tumour. After a liver biopsy the patient is diagnosed with unfavourable (subtype) carcinoma of unknown primary (CUP). You wish to undertake genomic testing and are considering which constitutional (germline) and/or somatic (tumour) genomic testing is available and appropriate for her.

Constitutional (germline) testing

• Patients who are considered for palliative chemotherapy with capecitabine should undergo constitutional (germline) testing of the dihydropyrimidine dehydrogenase (DPYD) gene. Certain variants in this gene result in a deficiency of the enzyme dihydropyrimidine dehydrogenase (DPD) and a subsequent reduction in metabolism of fluoropyrimidine-based chemotherapies such as 5FU and capecitabine. This results in serious and sometimes life-threatening toxicity, including diarrhoea, mucositis and skin reactions, if these chemotherapy agents are given at standard doses.
• No targeted constitutional (germline) genomic testing is specifically recommended for patients with CUP, but patients are eligible for paired constitutional and somatic (tumour-based) whole genome sequencing (WGS).

Somatic (tumour) testing

• The mutational profile of unfavourable CUP has been investigated in a number of clinical trials. TP53 variants are found in approximately 50% of unfavourable CUPs. Beyond this, CUPs demonstrate a very heterogeneous mutational landscape, with a diverse set of potentially actionable genetic alterations.
• Initial data from the CUPISCO randomised trial, which assessed the clinical utility of massively parallel sequencing (sometimes called next-generation sequencing)-based management approaches in CUP, indicates a favourable impact on progression-free survival associated with a molecularly directed treatment approach. However, overall survival data are pending.
• Somatic (tumour) testing for NTRK1, NTRK2 and NTRK3 fusion genes is available within the NHS for CUP patients as a biomarker for treatment with an NTRK inhibitor when all other approved lines of treatment have been exhausted.
• Patients with CUP are eligible for NHS WGS at any time after diagnosis.
• Large-panel massively parallel sequencing somatic (tumour) testing for CUP may be available within clinical trials.

• Consult the National Genomic Test Directory to ensure your patient is eligible for testing. You can also refer to a spreadsheet containing details of all available tests.
• To find out which genes are included on different gene panels for constitutional (germline) testing, see the NHS Genomic Medicine Service Signed Off Panels Resource.

Constitutional (germline) testing

• Patients being considered for palliative chemotherapy with capecitabine should undergo constitutional (germline) DPYD testing using test code M226.3.
• For constitutional (germline) DNA-based tests (all the above listed tests), an EDTA blood sample is required. Please refer to your local Genomic Laboratory Hub (GLH) for details of test request forms and where to send samples.

Somatic (tumour) testing

• NTRK fusion gene analysis can be requested as test M226.1. This consists of massively parallel sequencing structural variant analysis.
• WGS of CUP is requested as code M226.4. WGS requires access to a fresh tumour sample and a matched blood (EDTA) sample for constitutional (germline) testing. A record of discussion form must be completed for this investigation. Please discuss the case with your local GLH before submitting samples for WGS to confirm the local test pathway details.
• Information about patient eligibility and test indications was correct at the time of writing. When requesting a test, please refer to the National Genomic Test Directory to confirm the right test for your patient.

For clinicians

• NHS England: National Genomic Test Directory (note that somatic (tumour) tests are listed in the directory for cancer, while constitutional (germline) tests are listed in the directory for rare and inherited disease)
• NICE: Entrectinib for treating NTRK fusion-positive solid tumours
• NICE: Larotrectinib for treating NTRK fusion-positive solid tumours
• UK Chemotherapy Board: Personalised medicine approach for fluoropyrimidine-based therapies (PDF, eight pages)

References:

• Krämer A, Bochtler T, Pauli C and others. ‘Cancer of unknown primary: ESMO clinical practice guideline for diagnosis, treatment and follow-up‘. Annals of Oncology 2022: volume 34, issue 3, pages 228–246. DOI: 10.1016/j.annonc.2022.11.013
• Mileshkin L, Bochtler T, Pauli C and others. ‘LBA16 primary analysis of efficacy and safety in the CUPISCO trial: A randomised, global study of targeted therapy or cancer immunotherapy guided by comprehensive genomic profiling (CGP) vs platinum-based chemotherapy (CTX) in newly diagnosed, unfavourable cancer of unknown primary (CUP)‘. Annals of Oncology 2023: volume 34, supplement 2, pages S1,254–S1,335. DOI: 10.1016/j.annonc.2023.10.006

For patients

• Cancer Research UK: What is cancer of unknown primary?
• Macmillan Cancer Support: Cancer of unknown primary (CUP)